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Intro to Data Analysis

Utah Valley University - BIOL3100

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Course Syllabus

Shared Course Notes

(Anyone with link can edit)

The philosophy of this course

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Table of Contents

Week 1 | Week 5 | Week 9 | Week 13

Week 2 | Week 6 | Week 10 | Week 14

Week 3 | Week 7 | Week 11 | Week 15

Week 4 | Week 8 | Week 12 | Week 16

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The Command Line, File Paths, Git

Week 1

Topics:

• Installing Software | Command-line | Git version control

Assignments

• Read: What is Git all about?
• Install Git, R, and R-Studio on your laptop (part of Assignment 1)
• Be ready to explain what Git, R, and R-Studio are.
• Do Assignment 1 and upload a link to your new GitHub account to Canvas.
• Take a look at this document to see where this class is going

Resources

• Download Git
• Download R
• Download R-Studio
• Navigating with the command line
• Basic Git Commands
• Git Cheat Sheet
• Git tutorial for beginners
• Best Git Cheat Sheet Ever!

Practice

• Make 10 separate changes and commits to your README.md file and push each one to GitHub

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Week 2

Topics

• File paths | Pipes | Redirection | Wildcards | Essential Unix Commands | Parameters

Assignments

• Assignment 2

Resources

• The Two Cultures of Computing and how to get over your fear of coding
• Remedial Unix Shell
• Basic Unix Commands
• Very Useful Tutorial
• On the Value of Command-Line Bullshittery
• On the Annoyance of Command-Line Bullshittery
• So is this stuff even useful for bioinformatics? YES!

Practice

• Exercise 1
• Exercise 2
• Shell find exercise

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Getting to Know R

Week 3

Topics

• R Data types and conversions | Reading and Writing Files | For-Loops | Packages and Projects

Assignments

• Assignment 3
• Assignment 4

Resources

• Data Types in R
• For-Loops
• Reading data into R
• R Projects

Practice

• Vectors
• Factors
• Characters
• Regular Sequences
• Indexing
• Missing Values
• Loops in R

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Week 4

Topics

• Logical Operations | Subsetting | “Grammar of Graphics” ggplot Intro

Assignments

• Read through the materials in the Resources section below
• Assignment 5
• Exam 1

Resources

• Subsetting
• More Subsetting (It’s important!)
• Operators

Practice

• Logical Operations
• Find a new built-in data set in R. Use several methods to subset it over and over until you are an expert!
• Out-of-order Code

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Visualizing a Data Set

Week 5

Topics

• ggplot | patchwork | ggforce

Assignments

• Assignment 6
• Ugly plot contest!

Resources

• ggplot Introduction
• More ggplot
• ggforce
• patchwork
• Extensive ggplot2 Tutorial
• How to plot anything in ggplot part 1 | part 2 (This is a GOOD thing to watch!)

Practice

• Out-of-order Plotting Code
• ggplot Examples
• ggplot Shiny App Lets you use GUI to see ggplot code.

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Clean and Transform Data

Week 6

Topics

• Tidy Data | dplyr verbs | tidyr verbs

Assignments

• Read this paper: Tidy Data
• Assignment 7

Resources

• Tidy Data Chapter
• Transforming Data Frames
• dplyr Verbs
• tidyr Verbs
• tidyverse Cheat Sheet

Practice

• BioLog Challenge
• Out-of-order Code
• Out-of-order Code2

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Week 7

Topics

• Data Wrangling | Joins | The Curse of Other Peoples’ Data

Assignments

• Read This Handout
• Read This Paper
• Create a validated Excel Spreadsheet for data collection for the experiment we design in class
• Exam 2

Resources

• Data Wrangling Chapter
• Wrangling Cheat Sheet
• Visual Explanations of Joins

Practice

• Download this spreadsheet. See if you figure out all the things wrong with it.
• Error Sleuth Practice
• Data Entry Case Study

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Getting More From R

Week 8

Topics

• Writing Functions | Conditional Execution | source()

Assignments - Watch this video from Jenny Bryan about debugging

Resources

• Functions
• Conditional Execution

Practice

• Write a function that returns the min, max, and mean of any set of real numbers
• Write a function that takes a data frame and returns a new data frame with one random column removed
• Write a function that takes a data frame… if there are more than 3 columns, your function should return the column names as-is; if there are 3 or fewer columns, your function should return the column names in reverse order.
• Write a useful function that you might want to use in the future (your choice)
• Put all of these functions into a new R script and save it in your main data course repository
• In a new empty R script, call your functions with source() and test them out

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Model Building and Testing

Week 9

Topics

• Building and Testing Models

Assignments

• Assignment 8

Resources

• Modeling Intro
• Model Basics
• Model Fitting

Practice

• Building Models Example
• Intro to Hypothesis Testing
• Cross-Validation and Logistic Regression

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Week 10

Topics

• More models | Statistical Tests

Assignments

Resources

• Linear Regression
• More Linear Regression
• Common Statistical Tests
• Mixed-effect Models
• Everything is a Regression _ Introduction to mixed effects models This is a VERY good paper.

Practice

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Communicating Your Results

Week 11

Topics

• R-Markdown | Reproducible Reports

Assignments

• Assignment 9

Resources

• Intro to R Markdown
• Markdown Live Preview Generator
• Expert-Level Markdown Project

Practice

• Using the resources above, generate a markdown document that analyzes the “iris” data set and push it to a new GitHub repository named Iris_Markdown
• Play with options and code to create a document that looks good and presents your analysis and results clearly
• This is similar to Assignment_9, but I’m asking for a brand new “Iris_Markdown” repository that is self-contained.

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Week 12

Topics

• Proper Project Organization | Collaboration

Assignments

• Peer evaluation of Assignment 9 (Organization, Portability, Accuracy, Understandablity)
• Exam 3

Resources

• Project-oriented Workflows
• Reproducible, Portable, Self-Contained
• Proper Project Organization Example
• Another, More Detailed Example
• Project organization part 1 video
• Project organization part 2 video

Practice

• Peer evaluations of Iris_Markdown repositories (from last week); Clean them up and make them more organized

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Putting it all together

Week 13

Topics

• Data Analysis from raw to report

Assignments

• We will work together in class to do a complete analysis in real-time

Resources

• Benefits of Live Coding

Practice

• Analyze the “esoph” data set and generate a markdown report

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Week 14

Topics

• Building a website with GitHub and R-Markdown

Assignments

• Work on Final Project
• Create a GitHub Personal Website
• Upload a brief CV and the updated (improved) html of Assignment 9 to your new website

Resources

• GitHub Pages
• Here’s the GitHub repository for this course website
• Rmarkdown to web page walkthrough video
• Reproducible workflow video

Practice

• Go through my course website repository (link above) and try to relate the code there to the html version of the website your internet browser is displays

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Week 15

Topics

• TBD

Assignments

• Work on Final Project

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Week 16

Topics

• TBD

Assignments

• Exam 4 (Redo any previous exam to replace it’s score)

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‘Luck is statistics taken personally.’ – Penn Jillette